Biology subjects

Pett-Ridge, J.

Publications and source records attributed to Pett-Ridge, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Saprotrophic soil fungus dissolves lithium lepidolite through inositol rescue metabolism

Microbial weathering of minerals represents a key biogeochemical process through which microorganisms access essential nutrients locked within rock and ore substrates. In this study, we investigated the metabolic response of a model fungus during growth on lithium (Li) ore to elucidate the mechanisms underpinning biologically mediated mineral weathering and subsequent metal mobilization. Our results revealed a distinct metabolic shift in the fungus when cultivated on Li ore, characterized by altered patterns of organic acid production and energy metabolism. This shift coincided with measurable weathering of the Li ore matrix and the consequent release of soluble Li into the surrounding environment, demonstrating a direct link between fungal metabolic reprogramming and mineral breakdown. Importantly, these observations are consistent with metabolic shifts documented in previous studies of mineral weathering by this fungus, suggesting that such responses constitute a conserved and reproducible strategy employed during the colonization of mineral substrates. Although the present work was conducted using a single model microorganism under controlled conditions, the findings carry broader ecological implications. Natural microbial communities inhabiting mineral-rich environments may undergo analogous metabolic shifts when weathering minerals to acquire limiting nutrients, thereby contributing to large-scale elemental cycling and metal release. Understanding these processes not only advances fundamental knowledge of microbe-mineral interactions but also informs emerging applications in biomining and bio-based recovery of critical metals such as lithium. Collectively, this study highlights the central role of microbial metabolism in driving mineral weathering and offers a framework for predicting and harnessing similar processes within complex microbial communities. IMPORTANCEThe model fungus exhibits a distinct, reproducible shift in metabolism--particularly in organic acid production and energy pathways--when grown on Li ore, directly linking cellular metabolism to mineral breakdown. This metabolic shift promotes weathering of the ore matrix and the release of soluble lithium, demonstrating a biological route for liberating a critical metal from its mineral host. Because similar shifts occur across different minerals, natural microbial communities likely employ comparable strategies to weather minerals and acquire limiting nutrients, contributing to global elemental cycling. These findings provide a foundation for sustainable biomining and bio-based recovery of lithium and other critical metals, offering a lower-impact alternative to conventional extraction methods.

microbiology↗

bioRxiv2026

Microbial communities in tropical soils are highly resilient to fluctuating redox conditions

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

microbiology↗

bioRxiv2026

Drought Dominates Engineered Lipid Sink Effects on Sorghum Physiology and Carbon Allocation

Determining the environmental limits that govern how engineered metabolic traits control whole-plant carbon (C) allocation is essential for developing climate-resilient bioenergy systems. Oil-enhanced sorghum offers a promising strategy to boost aboveground energy density, yet its system-wide effects on root C investment and soil C delivery, particularly under drought, are largely uncharacterized. Here, we provide the first comprehensive assessment of these interactions using whole-plant 13CO2 continuous labeling, depth-specific sampling of roots and rhizosphere soil, and coordinated measurements of photosynthesis, stomatal anatomy, tissue nitrogen, and root non-structural carbohydrates (NSCs). Under well-watered conditions, oil enhancement produced distinct aboveground physiological changes, including slightly longer stomata, lower stomatal density, significantly higher leaf nitrogen concentration and biomass, and greater leaf 13C enrichment. Importantly, these aboveground changes did not translate into detectable shifts in the allocation of recent photosynthate to belowground pools. In contrast, drought acted as a dominant regulatory factor, reorganizing C flow across both genotypes by suppressing photosynthesis and leaf water status, increasing root nitrogen and NSC reserves, and significantly promoting the retention of recent assimilates in shallow root systems. Depth-specific 13C patterns showed that drought reduced new C incorporation into deep roots while increasing 13C enrichment in deep rhizosphere soil, suggesting that drought altered the balance between C investment in root growth and rhizodeposit C inputs at depth. Ultimately, soil moisture availability was an overriding determinant of belowground C partitioning and vertical C delivery, superseding the influence of the engineered lipid sink. These findings provide new mechanistic insight into the environmental constraints on C flow in an engineered bioenergy crop and identify moisture-driven limitations as the primary bottleneck for translating synthetic metabolic innovations into robust, ecosystem-level C outcomes.

ecology↗

bioRxiv2026

Microbial autotrophy is widespread across soils and most prevalent in deep and saturated environments

Genes for CO2 fixation occur in soil microorganisms, but little is known about the pathways that are most common across ecosystem types, the organisms with these genes, where different CO2 fixation pathways are most prevalent, and the energy sources that support autotrophy across ecosystems. Here, we investigated microbial capacity for autotrophy in soils using 853 metagenomes and 201 metatranscriptomes from a wide range of terrestrial ecosystems (agricultural soils, wetlands, weathering rock). Autotrophy-associated RuBisCO (Form I and II) is widely encoded across all soils and occurs in bacteria from numerous lineages (38 phyla). RuBisCO Form IE is consistently more phylogenetically diverse in soils than in marine ecosystems, suggesting that it may have evolved to function in soil-like environments. A newly discovered deeply branching Form I RuBisCO, Form I, supports the hypothesis that Form I RuBisCO originated in anaerobic environments. Further, saturated soils harbor more, and more distinct, autotrophic microbes, many of which may use the Calvin-Benson-Bassham cycle or Wood-Ljungdahl pathway for CO2 fixation. Overall, the results indicate that autotrophy is a particularly important metabolism in deep, saturated soils and weathering rock.

microbiology↗

bioRxiv2026

Divergent successional patterns and infection dynamics in virion and transcriptionally active soil viral communities following phosphorus amendment and wet-up

Viruses are key regulators of terrestrial carbon, nitrogen, and phosphorus cycling, yet how environmental perturbations structure viral activity remains poorly resolved. Rewetting of seasonally dry soils triggers rapid microbial and viral responses, but the relationships between virion-associated and transcriptionally active viral communities, and the role of phosphorus in these dynamics, remain unclear. Here, we integrated viromics, metatranscriptomics, environmental DNA (eDNA), and amplicon sequencing to track viral succession and virus-host interactions over three weeks following soil rewetting, with and without phosphorus amendment. We identified 13,840 viral populations (vOTUs), of which 3,803 were transcriptionally active, representing ongoing infections. Wet-up significantly altered virion and transcriptionally active viral communities, while phosphorus selectively influenced prokaryotic and transcriptionally active viral communities but not virion composition. Virus-host linkages were predicted for 32% of vOTUs, with transcriptionally active bacteriophages infecting Actinomycetota increasing under phosphorus amendment. Following wet-up, virion abundance decreased [~]3-fold while virocells increased [~]5-fold, indicating a shift from viral persistence in dry soils to active infection. Phosphorus further enhanced virocell abundance. eDNA captured rapid viral turnover and revealed transient dynamics not resolved by viromes or metatranscriptomes alone. Together, these results demonstrate that soil viral communities are structured by distinct but complementary molecular pools that operate over different ecological timescales. Wet-up activates a reservoir of persistent virions, while phosphorus availability regulates infection dynamics and host-virus coupling. These findings highlight viruses as dynamic drivers of microbial turnover and nutrient cycling following environmental perturbation, advancing a more predictive understanding of soil ecosystem responses to changing resource availability.

ecology↗

bioRxiv2026

Reduced precipitation alters microbial availability and redistribution of rhizosphere carbon

Climate change intensifies grassland drying, which is predicted to decrease soil organic carbon (SOC) storage. Yet how reduced soil water affects the transport and processing of carbon in the rhizosphere -- a major source of SOC supporting microbial activities -- remains poorly resolved under field conditions. We traced living root-derived carbon (rhizodeposit C) into soils and microbes using {superscript 1}3CO2 labeling in a multi-year precipitation manipulation experiment in a California Mediterranean annual grassland dominated by Avena barbata. Under halved precipitation, season-averaged soil water content was 20% lower and soil matric potential more than threefold lower, without inducing detectable signs of plant stress. Quantitative stable isotope probing (qSIP) of rhizosphere microbial DNA revealed that up to 68% more bacterial and 13% more fungal taxa incorporated rhizodeposit C, and that microbial uptake of rhizodeposit C increased more over time under reduced precipitation, even as total microbial biomass and community composition were unchanged. {superscript 1}3C-informed co-occurrence networks of these consumers were larger and more connected under reduced precipitation. The surrounding soils contained less 13C, and modeled solute transport by soil water was 32-40% lower, implying that rhizodeposit C was retained and intensively processed nearer to roots rather than transported to the wider soil matrix. Our evidence supports that reduced precipitation concentrates rhizodeposit C near roots, increasing the number of distinct consumers and intensifying associations among them. This represents an overlooked mechanism linking precipitation reduction to rhizodeposit C cycling. These findings show that precipitation reduction may reshape rhizosphere C processing before apparent plant stress response, with potential consequences for the fate of rhizodeposit C in grassland soils.

microbiology↗

bioRxiv2025

Spatial and depth structuring predominate over temporal variation in Mediterranean grassland soil viral communities

Viruses have the potential to influence microbial community structure and elemental cycling in soils, but it remains unclear how these communities are distributed across space and time, which can shape how they respond to environmental change and impact ecosystem processes. Mediterranean grasslands, with their pronounced seasonal moisture fluctuations, offer an ideal system to examine viral biogeography. While previous studies hint at spatial structuring and moisture controls on viral communities, temporal responses to seasonal moisture shifts have not been comprehensively investigated in situ. Here, we generated 59 viromes and leveraged 89 metagenomes from two Mediterranean grasslands to measure soil viral communities across horizontal space (sampling zone), depth, and key seasonal stages of the Mediterranean water year (e.g. plant productivity, dry down and wetup). Sampling zone was the dominant driver of viral community composition in viromes, with time secondarily explaining variation in viral communities. In contrast, viral richness and DNA yields varied primarily across time. Spatial structuring also emerged in viruses recovered from metagenomes, with depth having the strongest effect, followed by sampling zone. Environmental variables and predicted host distributions partially explained these patterns, but substantial variation remained unaccounted for, suggesting a role for dispersal limitation. Overall, soil viral communities were primarily structured by spatial factors, with temporal and environmental influences acting secondarily, highlighting the importance of fine-scale spatial dynamics in understanding viral ecology. Future studies should explicitly examine the role of dispersal limitation and fine-scale host-environment interactions to fully resolve drivers of soil viral biogeography.

ecology↗

bioRxiv2025

Shrub and Sedge Rhizosphere Communities Display Distinct Affinities Toward Exudates and Soil Organic Matter Degradation: a Quantitative Stable Isotope Probing Analysis

Warming temperatures are accelerating permafrost thaw and changing tundra vegetation, where woody shrubs are displacing sedges. Shrubs, such as Betula nana, and sedges, such as Eriophorum vaginatum, exhibit distinct life strategies including unique root-associated, or rhizosphere microbial communities. As permafrost thaws it unlocks previously unavailable carbon and nutrient sources resulting in deeper roots and a translocation of rhizosphere communities. Because permafrost microbial communities contain lower diversity and biomass than rhizosphere communities, the coalescence of rhizosphere and permafrost microbial communities could alter soil organic matter (SOM) degradation rates and increase greenhouse gas emissions. To identify metabolic strategies across distinct rhizosphere and permafrost microbial communities we conducted an isotope tracing incubation experiment. We inoculated thawed permafrost with shrub and sedge rhizosphere communities while adding exudates or water daily and compared this to an uninoculated control. After 46 days, we spiked samples with 18O enriched water or 13C enriched exudates and measured isotope incorporation into microbial DNA with quantitative stable isotope probing (qSIP). Our results indicate that exudate additions had little effect on uninoculated permafrost communities but the addition of exudates and rhizosphere inoculants had a compounding effect on respiration rates. We found that soils inoculated with shrub rhizosphere communities contained a mixture of exudate and SOM degraders while soils inoculated with sedge rhizosphere communities contained mainly SOM degraders. Finally, we found that individual microbial taxa exhibited maximum growth rates in one environment, which was a combination of microbial inoculant communities and exudate addition treatments. Our results reveal that microbial niches are strongly influenced by substrate preferences and community context, and suggest that a reduction in sedges and an expansion of shrubs may provide a mechanism by which permafrost carbon losses are mitigated through corresponding shifts in microbial communities and their substrate preferences.

microbiology↗

bioRxiv2025

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland

Changes in global patterns can leave a lasting legacy in semi-arid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn--a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O, and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux; measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing; and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by [~]1 order of magnitude, yielding decreased community growth efficiency (CGE = gross community growth/net respiration), and microbial mortality declined by [~]2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover), this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low-CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting. Persistent decreases in CGE due to reduced winter rainfall result in consistent carbon loss as CO2, which, if sustained over multiple years, could ultimately lead to a net decline in total soil organic carbon.

microbiology↗

bioRxiv2025

Assessing the Potential of Switchgrass (Panicum virgatum L.) for Storing Carbon Belowground: Insights from a Multi-Site US Study

Agricultural intensification depletes belowground carbon (C) stocks, partly due to the exclusion of deep-rooted perennial species from landscapes where they were once dominant. Reintroducing deep-rooted perennials to cultivated land may help to mitigate SOC loss and restore ecosystem function. We quantified the effect of replacing shallow-rooted annual crops with a deep-rooted perennial grass, switchgrass (Panicum virgatum L.), by comparing 10 to 30 year-old switchgrass stands with paired annual row crop fields across the central and eastern USA. We hypothesized that switchgrass would store more root C and SOC than neighboring shallow-rooted annual crops, and that these effects would extend deeper than 30 cm. We also evaluated whether switchgrass stimulates decomposition of SOC at depth using radiocarbon (14C) to quantify replacement of slow cycling isotopically depleted SOC. Finally, we explored whether the effect of switchgrass on SOC is moderated by soil chemical and physical properties. While the effect of switchgrass on SOC in the surface 100 cm was positive at most sites, the average effect was highly uncertain and statistically indistinguishable from zero (mean difference in SOC = 0.6 kg C m-2 [95% CI -0.8 to +1.9 kg C m-2]). By contrast, we found that root biomass C was consistently more deeply distributed and more abundant under switchgrass, yielding an estimated additional 0.6 kg C m-2 in the surface 100 cm of soil under switchgrass [95% CI +0.5 to +0.7 kg C m-2]. 14C measurements suggested that root C inputs were adding to existing SOC without stimulating decomposition. The effect of switchgrass on belowground C was not strongly related to any of the environmental factors that we evaluated. Our observations show that root biomass C can contribute substantially to belowground C stocks when deep-rooted perennial grasses replace shallow-rooted annual crops.

ecology↗

bioRxiv2025

Internal DNA standards for Isopycnic Centrifugation of Environmental DNA in Quantitative Stable Isotope Probing

Element assimilation rates or the DNA replication rate of microbial taxa can be measured in environmental samples through quantitative DNA-stable isotope probing (DNA-qSIP). Here, we introduce a set of DNA standards that may be used to quantify the density of DNA extracted from environmental samples after isopycnic centrifugation. The standards are approximately 9 Kbp PCR products with either isotopically enriched (98 atom% 15N, 13C) nucleotides or natural abundance nucleotides and have densities that differ by 0.051 g/mL. The internal standards were tested in a DNA-qSIP analysis of bacterial populations in soil exposed to 63 atom% H218O, performed in two different laboratories with different equipment and protocols. While fractionation results, including number of fractions taken and differences in density between adjacent fractions, between the two laboratories were different, the internal standards allowed the two data sets to be compared, and both research groups found similar Excess Atom Fraction (EAF) of oxygen-18 in the DNA of bacterial taxa. These internal DNA standards allow direct comparison of DNA-qSIP results from different experiments regardless of operator, tracer enrichment levels, protocol or equipment used and can support the creation of a large global database that contains qSIP results from many different laboratories. ImportanceDNA-qSIP is an important technique in microbial ecology that allows the growth and nutrient assimilation rates of microbial taxa, including those that have not yet been cultured, to be measured. Growth and assimilation rates are extremely variable parameters in microbial ecology because most of the microbial community is dormant and inactive, which complicates linking microbial populations to ecosystem processes. DNA-qSIP is increasingly practiced in a range of laboratories, using different equipment, isotopes, substrates, and protocols, making comparison of results among different research groups challenging. Here we describe the development of internal standards, 2 pieces of DNA with different isotopic content and hence buoyant density, that can be added to environmental DNA before isopycnic centrifugation. Our results show the internal DNA standards allow DNA-qSIP results to be compared across laboratories and could contribute to the formation of a large DNA-qSIP database that contains growth or nutrient assimilation rates of microbial taxa from many different experiments.

microbiology↗

bioRxiv2025

Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a grassland soil

Drought effects are pervasive in many terrestrial ecosystems, yet little is known about the impact of drought on the transformation of plant C inputs to mineral-associated organic matter (MAOM) - the largest and slowest-cycling pool of organic carbon (C) on land. Using 13C-CO2 greenhouse labeling chambers, we tracked the formation of 13C-MAOM derived from Avena barbata living root inputs (13C-rhizodeposits) versus A. barbata decaying root inputs (13C-root detritus) under normal moisture and spring drought conditions in a semi-arid grassland soil, and then tested the durability of this 13C-MAOM in a subsequent persistence assay. Overall, drought reduced formation of MAOM - both per gram of soil and across the entire soil profile. Notably, drought conditions enhanced the persistence of MAOM derived from root detritus, though not of MAOM derived from rhizodeposition. Drought had the most pronounced effect on MAOM accrual from rhizodeposition late in plant development (week 12) whereas it had the most pronounced effect on MAOM accrual from root detritus early in root decomposition (week 4). These temporal responses were associated with distinct trajectories in microbial community-level growth rates, the average mass of OM compounds, and the number of unique metabolites within each habitat. Our results provide mechanistic evidence that drought reduces overall formation of MAOM but can enhance its persistence in a grassland soil.

ecology↗

bioRxiv2025

Tracking Persistence and Dynamics of Active Soil Viruses with SIP-Viromics

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied a genome-resolved stable isotope probing viromics (SIP-viromics) approach, combining H 18O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined metagenome assemblies. Only 22% of vOTUs exhibited significant 18O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 x 1010 to 6.59 x 1010 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota--bacterial groups known to rapidly resuscitate following rewetting--suggesting that some viruses exhibit rapid turnover while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal host-associated patterns of lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. ImportanceUnderstanding the persistence and production dynamics of soil viruses is critical for elucidating their roles in microbial community dynamics and nutrient cycling, yet these processes have remained largely uncharacterized due to methodological limitations. By integrating stable isotope probing with viromics, this study provides a robust framework for directly distinguishing newly produced from persistent virions in situ. Unlike conventional viromics, which only catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence under natural soil conditions. Our results demonstrate that most virions in a seasonally dry soil persisted through a rewetting event, with active replication limited to a minority of viral populations. Persistent virions were primarily linked to dominant bacterial groups, indicating that host ecophysiology and environmental stability strongly influence lytic infection. Collectively, these findings highlight viruses as long-term reservoirs of genetic material, capable of shaping microbial dynamics and ecosystem processes over time. This work establishes SIP-viromics as a powerful approach for studying virus-host interactions and their ecological significance in terrestrial environments.

microbiology↗

bioRxiv2025

Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats

Microbial ecological strategies are shaped by a fundamental trade-off: is it better to specialize and thrive in a narrow niche or generalize and persist across diverse environments? In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere, where microorganisms encounter distinct resource inputs from living and decaying roots. Using H {superscript 1} O quantitative stable isotope probing (qSIP), we measured in situ bacterial and fungal growth rates in the rhizosphere, the root detritusphere, and in the combined presence of rhizosphere + root detritus to test whether specialists--microbes growing in a single habitat--grow faster than generalists that persist across multiple environments. Specialists grew consistently faster than generalists, suggesting a trade-off between the breadth of environmental conditions a microorganism can tolerate and its ability to grow quickly in a specific habitat. This cost to broad niche adaptation was apparent for bacteria, but growth rates of fungal saprotrophs varied little between specialists and generalists, reflecting how fundamental differences in life-history strategies between bacteria and fungi can shape microbial responses to resource availability and habitat heterogeneity. Net relatedness and nearest taxon indices indicated total bacterial communities were phylogenetically clustered while specialist and generalist communities were phylogenetically random, suggesting that functional traits, not lineage, best predict ecological strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay is key to predicting soil-carbon trajectories.

microbiology↗

bioRxiv2025

Composition, growth, succession, and function in the Cladophora microbiome: insights from quantitative Stable Isotope Probing and NanoSIMS imaging

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. We characterized successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulfur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulfur bacteria (bacteria that reduce or oxidize sulfur/sulfates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

microbiology↗

bioRxiv2024

The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts

Mediterranean grasslands, vital natural and agricultural ecosystems, experience seasonal variation in water content that likely affect microbial activity. We used metagenomics-informed stable isotope probing to investigate how the activities of microorganisms in Angelo Reserve (2160 mm rainfall) and Hopland (956 mm rainfall) soil change over depth and the seasons. At both sites, we find that the relative abundances of organisms in shallow soil changes relatively little but the most abundant organisms vary greatly with soil depth. Notably the highest levels of isotope incorporation, indicative of growth, occurs in deep soils. The active part of the 0-10 cm soil community varies over time, especially in Hopland soils during the fall rewetting. We defined a large, novel clade of Actinomycetota with notable capacity for thiosulfate oxidation whose representatives are prevalent and active in deep soils (>20 cm) across both ecosystems. Active Saccharibacteria unexpectedly encode nucleotide synthesis genes that enabled isotope incorporation while growing in shallow Angelo soils over all time periods. In contrast to predicted episymbiotic lifestyles of Saccharibacteria, other highly active bacteria are predicted predators. Obligately predatory Pseudobdellovibrio are active in intermediate depth Hopland soils whereas bacteria of the order Haliangiales are active in shallow Angelo soils. Supporting predatory lifestyles of Haliangiales, we used in silico structure prediction to assemble a large protein complex that we identify as a contractile injection system. Overall, the results indicate the potential for active carbon turnover in deep grassland soil and strong seasonal changes in the active members of microbial communities, despite relatively minor shifts in community composition.

bioinformatics↗

bioRxiv2024

Phosphate amendment drives bloom of RNA viruses after soil wet-up

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting--while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2,190 RNA viral populations were identified across five phyla, with 37% of these predicted to infect bacteria (26%) or fungi (11%). Only 1.2% of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages, particularly Leviviricetes, proliferated significantly. Notably, 60% of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 107-109 bacteria per gram of soil, aligning with the total bacterial population (107-1010 g-1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect. HighlightsO_LISoil wet-up influences RNA virus dynamics for over a week C_LIO_LIThe majority of hosts predicted for RNA viruses were bacteria and fungi C_LIO_LIPhosphate amendment preferentially supports Lenarviricota over other RNA viruses C_LIO_LI60% of vOTUs that responded to phosphate were from unknown bacteriophage clades C_LIO_LIMost soil bacteria are predicted to be infected by RNA bacteriophages within a week C_LI

microbiology↗

bioRxiv2024

Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils

BackgroundWet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment--driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable. ResultsTo investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with 13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were 13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phyla Pseudomonadota, Acidobacteriota, and Actinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions. ConclusionsOur study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.

microbiology↗